[BioC] chrome coordinates are not same between Ensembl and Affy's annotation file

[shirley zhang]

Hi James,

Thank you vey much for your quick reply.

Yes. You are right, Affy's annotation is based on NCBI build 36. Do
you know which version of Ensembl is close to Affy's annotation? Since
I have the coordinates for many probes from Affy's exon array, it
would be much easier for me to map Affy's probe location to
Ensemble's.

Thanks again,
Shirley


On Thu, Sep 24, 2009 at 2:52 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> Hi Shirley,
>
> shirley zhang wrote:
>>
>> Dear List,
>>
>> I have been trying to draw the genome graphs for some genes in human.
>> I found that the coordinates of some genes are not close between
>> Ensembl and Affy's annotation (Affymetrix Human Exon array). For
>> example, gene SFRS1:
>>
>> SFRS1 (ENSG00000136450):     Chromosome 17: 56,078,284-56,084,707
>> reverse strand  (Ensemble 55)
>>
>> SFRS1Transcript Cluster ID: 3764103  Human Exon 1.0 ST):
>> chr17:53421412-53439635 (-)
>>
>> Can anybody tell me what happens?
>
> Sure. Things change. If you query the UCSC genome browser using NCBI build
> 36, you get
>
> SFRS1 (uc002ivj.1) at chr17:53433279-53439706 - splicing factor,
> arginine/serine-rich 1 isoform
> SFRS1 (uc002ivi.1) at chr17:53433279-53439706 - splicing factor,
> arginine/serine-rich 1 isoform
>
>
> If you then try the newer build (GRCh37) you get
>
> SFRS1 at chr17:56078282-56084707 - (NM_006924) splicing factor,
> arginine/serine-rich 1 isoform
> SFRS1 at chr17:56078282-56084707 - (NM_001078166) splicing factor,
> arginine/serine-rich 1 isoform
>
> The affy annotation is based on older information than Ensembl.
>
>
> Best,
>
> Jim
>
>
>>
>> Thanks,
>> Shirley
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>



-- 
Xiaoling (Shirley) Zhang

Ph.D. Candidate in Bioinformatics
Boston University, Boston, MA
Tel: (857) 233-9862	
Email: zhangxl at bu.edu